Metroid Fusion: The Federation Strikes Back
by HopefulToad
Summary: Samus Aran's alliance with the Galactic Federation is upended following the events of Metroid Fusion, leaving her as a wanted fugitive. In her efforts to keep herself, computer Adam, and the etecoons and dachoras alive, she becomes allies with the unexpected.
1. Calm After the Storm

Calm After the Storm

For the first time since setting foot on the Biologic Space Labs research station, Samus could relax.

Or at least, she would have been able to relax, if she could actually take off her Power Suit. Thanks to it being permanently fused with her body after she was infected by the X, that was no longer an option.

She sat in the pilot seat of her "borrowed" Galactic Federation space ship. Only a few minutes ago, she had narrowly escaped being vaporized in the massive explosion that left the B.S.L. station, the X parasites, and the entire planet of SR388 as cosmic dust. Now, her ship was on a course to nowhere in particular.

If things had gone normally, at this point she would contact the Federation to inform them of a job well done, then maybe arrange to buy this ship from them for permanent use, seeing as her own ship had been destroyed not too long ago. But she doubted the Federation would be happy to hear her mission report this time.

"Adam," Samus said, "how will the Federation react when they find out what happened?"

The robotic voice of Adam, the AI formed from the uploaded brain of her late commanding officer, sounded from the ship's main speakers. "Not well. I had already informed them of your unauthorized access to the top-secret Metroid breeding laboratory, and that it was jettisoned and destroyed as a result of the SA-X following you into it. When they find out you ignored orders and crashed the station into SR388, you'll likely be charged for the destruction of a research station of immense monetary and scientific value, as well as the premeditated obliteration of an entire planet, also of scientific significance, which is a capital offense."

"Right. And what would become of you if I turned myself in?"

"I would be deactivated for going rogue."

"What about the Etecoons and Dachoras?"

"They would likely be retained for experimentation and study, or possibly euthanized."

"So, turning myself in isn't the best idea."

"I would think not."

"How long before they find out about the research station?"

"They already know. The station was broadcasting information about itself up until its destruction. They know someone piloted it into the planet. It's only a matter of time before they realize that it was us."

A screen came to life on the ship's HUD to the left of Samus. It read, "Incoming Transmission: Galactic Federation Officer John McMann".

For a brief moment, Samus considered accepting the transmission. Then she rejected it and shut down all long-range communication systems on the ship. She doubted there was anything she could say to appease them.

"Adam, can the federation track this ship?"

"I've disabled the built-in tracker, so that should buy us some time, but it would be best to get a new ship if you want to go a prolonged period without being accosted by federal agents."

"Set a course for the nearest trade port. I'm going to go clean myself off."

"Understood," Adam replied.

_How weird_, Samus thought, _for me to be giving the orders instead of him._ She stood up and exited the cabin, heading for the lower deck where the habitation quarters were. On the way, she passed by the corridor where the Etecoons and Dachoras were resting peacefully, the baby dachora asleep on top of its mother, and the three Etecoons curled up like puppies. One of them perked up as Samus walked by. It scampered over, happy to see her.

Samus couldn't help but smile. She had saved the lives of these creatures twice, and less than an hour earlier, they had returned the favor. With Adam's help, they piloted the ship away from the destructive path of the Omega Metroid, and then returned it in time for her to board it and escape the destruction of the B.S.L. station.

The Etecoon leapt onto Samus, clambered up her, and perched on her shoulder, looking proud of itself. With Etecoon in tow, Samus stepped onto the auto-lift, which lowered her down to the habitation deck.

It was a cramped area; not much room for comfort of living on a small ship built for short-term missions. A cot in the corner, a food preparation and storage area, and a washroom. Samus gently set the Etecoon down and stepped into the shower, still fully clothed in her orange and red Fusion Suit. She turned on the water and stood under it, rinsing off the grime, dust, and dirt that had accumulated on her suit during her time in the various simulated environments of the B.S.L. station.

The Etecoon watched her, curious. Then it stepped into the water stream cautiously and imitated Samus, turning around in the water and brushing various parts of itself off, to her amusement.

Samus lifted her visor, exposing her face to the ship's air. It was the only part of her body not restricted by the Fusion Suit. She rinsed her face under the water. The Etecoon tried the same, spluttering when it got water in its eyes and up its nose.

She shut off the water and switched on the shower's fans, drying her suit off. Internal fans situated within her suit evaporated any water remaining in the recess of her helmet. The Etecoon, standing in the warm air with her, rapidly became very fluffy, with its hair sticking out when it dried.

Samus stepped out of the shower and walked over to the cot. She was exhausted, and needed rest. Climbing into the cot, thankful that the inside of the suit was padded well, she settled in to sleep. The Etecoon, ever the copycat, jumped onto the bed and snuggled up against her suit. She didn't mind.


	2. Searching For a Ship

Searching For a Ship

Samus awoke to the sound of Adam's voice.

"Samus, we have arrived."

She got out of bed, still somewhat tired but feeling much better than before. Her movement stirred her Etecoon friend awake. He bounced off the bed and ran over to the auto-lift, stopping and patiently waiting as it carried him to the upper deck.

Samus checked the time readout on her HUD. It had been seven hours since she fell asleep.

She moved over to the auto-lift. The platform, sensing her awaiting it, moved down much quicker than it would with an occupant. She stepped on.

On the upper deck, the Etecoons and Dachoras were active, exploring and playing with each other. Samus entered the main cabin. Out the main viewport, a large, green and blue planet loomed.

"Planet GR-78," Adam said. "Home to many trading outposts. You'll likely be able to find a new ship here, but you won't want to stay long. This is a highly visible corner of the galaxy, and not a great hiding place."

"Noted," Samus said. "What about you? What if we can't find a ship you are compatible with?"

"Our priority should be finding you a ship _you_ can use. Whether or not I am compatible with its computer systems is a secondary concern at best."

"Not to me it isn't. We'll find a ship we can transfer you to."

"We may not have that luxury."

"If we don't find a ship you can use," Samus said, "then we'll look somewhere else. I won't accept other alternatives."

"Stubborn as always, Samus. I do not believe it is in your best interest to have that concern, but I am in no position to assert authority over you. You may do as you wish."

"I appreciate it, Adam. I have to say, it _does _feel nice not to be ordered around by you."

"I'm sure it does."

Samus took over the ship's controls, bringing it down toward the planet's surface. The ship rocketed across the sky, heading for a large city. As they approached, an incoming transmission lit up the HUD. It declared itself to be from city patrol. Samus accepted the transmission.

"State your purpose, or be detained upon landing," a gruff voice said over the speakers.

"I'm here to buy a ship," Samus said.

"You have a ship."

"I'm here to buy _another_ ship."

"Are there stolen goods aboard your ship?" the voice asked.

"No." Technically true, though the ship itself was another story.

"Your ship has an unidentified signature. It's been tampered with. Prepare to be searched." The transmission cut out.

_Uh oh_, Samus thought. "Adam?"

"Yes, lady?"

"Is this outpost Federation-controlled?"

"Yes."

"Then _why_," Samus asked, exasperated, "did you _bring_ us here?"

"Because I knew it was our best shot at finding a ship within 15 light years from SR388. And I didn't expect the security to be as... enthusiastic as it is."

"Well, you can probably thank us blowing up SR388 and the B.S.L. station for that. We need to get out of here, now."

"Agreed," Adam said. "A cursory inspection would be enough to reveal this ship as a stolen Federation vehicle."

Samus banked upward and laid on the thrusters, rapidly sending the ship out of the planet's atmosphere.

"We need to find a planet outside the reach of the Galactic Federation," Samus said. "Probably one that outlaws and criminals frequent."

"Good, we will fit right in."

"We might be on the wrong side of the law, but we did the right thing. You know it, or you wouldn't have helped me."

"The nearest unsavory hideout for thieves is about 35.42 light years away. A 32-hour trip at this ship's highest warp speed."

"Let's go there, then," Samus said.

"And the ship will have approximately 1.24 percent of its fuel remaining when we arrive."

"Well, then we'd better hope that it's the place for us."

* * *

Samus knew the Etecoons and Dachoras were probably hungry, so she went down to the food preparation area to see what they had. What did Etecoons and Dachoras eat? She had no idea.

She grabbed seven ration packs and warmed them up in the ship's small food heater. Emptying a couple of the packs into a blender, she mixed it up with water into an unappetizing-looking brown concoction, then stuck a long straw in it. Opening her visor, she threaded the top opening of the straw through and into her mouth, and drank her meal. It certainly didn't taste great, but since she was hungry, and had little other options for eating thanks to her Fusion Suit, she managed to gulp it down. Then she brought the other ration packs up to give to the creatures.

They crowded around her, eager to see what food she had. She opened the ration packs and laid them on the ground, where the Etecoons and Dachoras inspected them. Seeming pleased, they dug in. The Etecoons picked out the vegetables, leaving the meat, while the mother Dachora picked up bits of meat, eating some and feeding small pieces to her child. The two species seemed like a perfect match for their mutualistic relationship.

Samus laid out bowls of water for them to drink and left them to their meals.

* * *

"Welcome to Motley 5," Adam's voice sounded from within Samus's suit.

She stood in rain-drenched mud outside the ship, which had landed moments before. Visibility was poor. The moon, apparently, was plagued by nearly incessant rainstorms. It orbited a large gas giant with a highly varied, colorful appearance, and was numbered as the last of its five moons. While habitable, it was hardly ideal for living thanks to its weather, so it became a hub for criminals.

"The local establishment is about an hour-long walk from here," Adam said. "You should be able to make it in about two minutes."

Behind Samus, bands of light radiated down from the ship, and in a flash of light, the Etecoons and Dachoras appeared. They ventured out into the rain, somewhat cautiously.

"Will they come back to the ship?" Samus asked.

"Most likely," Adam replied. "They appear to be attached to you, and recognize you as a source of safety."

Samus took off running. The muddy ground hindered her a little, but with the help of her suit, she quickly attained speeds impossible for a normal human being. At the top of a hill, she leapt through the air, spinning, maintaining her impressive momentum, and before she hit the ground, she jumped in the air again. Thanks to the space jump ability she had recovered on the B.S.L. station, she could virtually fly through the air.

"Samus, you're getting close. Drop to the ground and resume walking normally to avoid drawing attention to yourself."

Samus complied, landing in the mud in a crouched position, with one knee to the ground. She stood up and began walking.

The building was hard to make out through the torrential downpour, but it looked vaguely cylinder-shaped, and only tall enough to house a single floor. There were no windows that Samus could see. As she got closer, a door on the right side of the building became visible. She approached it, and it slid open, revealing another door. She stepped into the small entryway and the first door slid shut. The alcove was dimly lit, with mud plastered against the walls and floor.

Just as Samus was wondering when the second door would open, a loud noise signalled a large fan embedded within the ceiling turning on. The fan blew for about ten seconds, whisking most of the muddy water off of her suit. Then the second door opened, and the inside of the building was revealed.

Dim lights on the ceiling illuminated a room full of somewhat dirty metal tables and chairs, some occupied, others empty. On the far side of the room, a counter formed a semicircle along the curved wall of the building, with multiple stools running parallel along it.

The occupants of the room were a diverse group. Some were human, others not. None gave her more than a passing glance, except one: a space pirate that was sitting at the left corner of the counter. It looked up, saw her, made a noise that sounded like a startled squawk, and bolted out the nearest side door.

Samus scanned the room, looking for any other immediate threats. While some of the pub's clients were definitely packing weaponry, and a couple were hulking aliens bristling with threatening-looking appendages, none were of overtly hostile demeanor toward her.

She approached the counter. The bartender, casually leaning against the inner side of the counter, had his eyes on the galactic news being broadcast on a few screens hanging from the ceiling, but turned to address Samus when she sat down on one of the stools. He was human, and looked to be in his early thirties, with a small, neatly trimmed beard and relaxed brown eyes.

"Sorry," he said. "I don't serve any drinks for, um, robots."

In response, Samus retracted her visor, revealing her eyes and part of her face.

"Oh, you're not a robot!" the bartender said. "And you're a girl, if I'm not mistaken."

"How perceptive," she said. "Can I get a drink now?"

"Alright," the bartender said, amused. "What can I get you?"

Samus ordered a drink, and the bartender prepared it and handed it to her.

"Do you have a straw?" Samus asked.

"Why do you need a straw?"

"To drink this."

"Can't you take your helmet off?"

"No."

"No?"

"No."

"_Really_?" the bartender said. "I don't believe you. Can you take the rest of the suit off?"

"No," Samus said, growing irritated. "Can you just get me a straw?"

"Alright, alright." He reached under the counter, grabbed a straw, and handed it to her. She used it to take a sip of her beverage. The bartender watched her, fascinated.

"What's your name?" he asked.

"None of your business."

"Alright, 'None of your business', good to meet you. My name's Kale."

Samus said nothing. A few minutes passed in silence.

"So," Kale said, "why can't you remove the suit?"

"It's fused parts of itself to my body."

"Interesting. Not saying I believe you, but interesting. Could it be surgically removed?"

"No."

"Okay." Suddenly, a smug look appeared on Kale's face, as if he had just thought of something that irrefutably proved she was lying. "If you can't take that suit off, then how do you poop?"

Samus smirked. What a childish question. "My suit has built-in waste disposal functionality, and that's all _you_ need to know."

"Hmm. Fair enough, I guess. Are you hot underneath that suit?"

"It's temperature-controlled."

"That's not what I meant."

Samus couldn't believe she was having this conversation. "We're done talking about this. Look, do you know of anyone I could buy a ship from?"

"You need a ship, huh?" Kale paused. "You certainly didn't get here without a ship, but you want a new one, so your current ship must be marked, and you're probably running from something. You're quite fascinating, you know that?"

"How nice. Answer the question."

"Well, everyone here has a ship, obviously, but they all sort of need them, so they're unlikely to let you buy one off them. And they certainly won't want to trade for your marked ship."

"Okay, then I'm done here." Samus stood up.

"Wait," Kale said. "I might still be able to help you. I get a lot of customers, I know a lot of people. But I'll need to know more about you before I can help you more."

Samus suddenly became aware that the atmosphere in the pub had shifted. The room was dead silent, and all eyes were on her.

_That can't be good_, she thought.

A quick search revealed the problem: on the news screens, breaking news had appeared, accompanied by a picture of Samus in her Fusion Suit in its original colors. The statement read: "Wanted: Samus Aran, criminal bounty hunter. 5,000,000,000 credit reward for her capture, 2,500,000,000 for her death. Samus Aran is extremely dangerous, and recently caused the destruction of planet SR388. Contact your local Galactic Federation officer for details."

"Samus," Adam said, audible only to her, "this is not good. You need to leave."

Kale had followed her gaze and read the screen, too. "Samus, huh? Nice name. I like your new paint job, too."

Samus turned back to look at the rest of the room, to find that the two side exits were blocked by the large, menacing aliens, and the main entrance was blocked by several clientele, all with weapons drawn.

Samus sighed. So much for making a quick exit.

"If you have to fight," Adam said, "use non-lethal force. These people are not your enemy. They just want the bounty."

"It _is_ quite the large sum," Samus replied. "They must really like what I did."

"We're taking you in," announced the de-facto leader of the now-hostile patrons of the pub, a dark-haired, muscled man pointing some sort of gun at her. "We'll kill you if we have to."

Samus didn't bother responding. After all, actions spoke louder than words. Her visor slammed shut in preparation for battle.


	3. Pub Hostilities

Pub Hostilities

Samus moved like lightning through the pub, using her limbs to strike her assailants. She could have cleared the room in short order using her projectile weaponry, but not without killing most of its occupants, so she had to resort to physical attacks.

There were about nine opponents in the room, Kale not included. He seemed to have disappeared behind the counter. Two were the ten-foot tall, dangerous looking aliens of unknown origin, still blocking the side doors. Five were human, four men and one woman, all doing their best to shoot Samus. One was a species of alien with four arms, each holding a gun, and one was a rather large bipedal lizard.

Samus grabbed the gun from the leader with her left hand and kicked him in the chest, toppling him over. Tossing the gun aside, she rounded on the other human attackers nearby, all of whom were shooting her. She felt the blasts as moderately painful impacts, but it wasn't enough to stop her. A flurry of strikes from her elbow, left fist, and arm cannon left the other four human attackers on the ground, groaning in pain and incapacitated. Then the lizard leapt onto Samus's back, digging its claws in, its weight causing her to stumble.

The lizard tried biting at her shoulder, but her armored Fusion Suit kept its teeth at bay. Samus struggled in vain to get the creature off her back, while to her right, the four-armed alien leveled each of its four guns at her and fired. The impact from the blasts sent her and the lizard tumbling over a nearby table, and the lizard lost its grip on her.

Samus scrambled upright and kicked the lizard in its midsection as it tried to do the same, launching it a good distance further away from her. She rolled into her morph ball form and shot across the room, coming to rest at the feet of the four-armed alien. The alien gaped at the orange ball. Samus uncoiled and slammed her left fist into the alien's gut. The alien doubled over, and Samus kicked it, sending it sprawling, its guns flying out of its hands. Then something heavy smashed into Samus's shoulders, a crushing blow that flattened her body to the ground.

Alarms went off in her suit, with red warning icons appearing on her HUD. That attack had caused some damage. Ignoring the sharp pain, she turned to face upward, still lying on the ground, revealing one of the hulking aliens looming over her, with its companion not far behind. They were almost as broad as they were wide, with spikes jutting out from their elbows, forearms and shoulders, and fists bigger than Samus's torso. The close one, leering menacingly, brought its arm up to strike again. Samus rolled aside just in time, and the alien's fist collided with the solid floor instead, leaving a thick spiderweb of cracks in the stone.

Samus decided it was time to relax her stance on not using weaponry. She leveled her arm cannon at the alien. Hatches opened along the cannon, revealing a primed missile. She fired.

The missile struck the alien in an icy explosion, sending it staggering back as a sheet of ice cocooned it, freezing it in place. The alien's companion roared in response, but immediately received its own missile to the chest, likewise encasing it in ice.

The pub was silent at last, except for groans of pain from Samus's downed assailants. Samus strode through the room, relieving her enemies of their weaponry. All the weapons gathered, she tossed them into a corner and destroyed them with a few blasts from her arm cannon.

"Hey, miss," someone called. Samus whirled and aimed at the source, which turned out to be Kale, who had suddenly reappeared behind the counter. Kale flinched.

"Whoa, easy there!" he said, raising both arms. "I don't want to hurt you. Doubt that I could, anyway."

Samus, still on edge from the fight, did not lower her weapon.

"Look," Kale began, "if you're done beating up all my customers, I believe we had a conversation to finish."

"No, I'm pretty sure it was over. You don't have a ship to offer, and you can't help me."

"Ah, see, you're wrong about that. I _can_ help you. Or, more specifically, I can direct you to someone that can help you. Maybe."

"_Maybe?_" Samus eyed the occupants of the room apprehensively, uneager for the fight to resume. A few were starting to get up, but thankfully the icy prisons entombing the alien colossi had yet to thaw. "You'd better be able to give me more than 'maybe'."

"How about 'probably'? That suit your tastes better?"

Samus turned to leave.

"Wait!" Kale called. "There's a guy. At least, I think he's a guy. Pretty famous around here. Not exactly chummy with the Federation, so I'm sure you'd get along. I know how to contact him."

"Then do it."

A few of the humans had stood up, and hastily exited the building, staying far away from where Samus was standing in the middle of the pub. The lizard, too, quit the establishment, not wanting to receive any more injuries.

"How do I contact you?" Kale asked.

"You have a transmitter?"

"Yeah." He pulled the device out of his pocket.

Samus focused on the transmitter in Kale's hand. Her suit scanned it and picked up its frequency. She tapped the side of her helmet, sending her contact information wirelessly over to the device, which lit up in response to receiving the information.

"That info won't work after 24 hours," Samus warned. "Better contact your friend quickly."

"Cool," Kale said. "See you around, Samus."

"Send anyone to attack me, and I'm coming after you personally once I've taken care of them."

Without waiting for Kale to respond, Samus left the pub.


End file.
